[BioC] parallel and GSVA

[David Iles]

Hi Robert,

Thanks for your prompt response.

Yes, setting parallel.sz=1 does work. Thanks for that. I have 8 cores available, so can I set parallel.sz=8?

Thanks

Dave

Dr David Iles
School of Biology
University of Leeds
Leeds LS2 9JT

d.e.iles at leeds.ac.uk





On 11 Jan 2013, at 13:11, Robert Castelo <robert.castelo at upf.edu> wrote:

> Dear David,
> 
> just to discard any other issue not related to the parallel execution in 
> your system, could you try to call the gsva() function adding the 
> argument parallel.sz=1? does it work?
> 
> cheers,
> robert.
> 
> On 01/11/2013 01:18 PM, David Iles wrote:
>> Hi Folks,
>> 
>> I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays. To familiarise myself with the GSVA code, I worked through the example in the vignette, but encountered the following issue...
>> 
>>> data(leukemia)
>>> data(c2BroadSets)
>>> library(parallel)
>>> filtered_eset<- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
>> +                           var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
>> +                           feature.exclude="^AFFX")
>>> leukemia_filtered_eset<- filtered_eset$eset
>>> leukemia_es<- gsva(leukemia_filtered_eset, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs
>> Mapping identifiers between gene sets and feature names
>>   |                                                                                                               |   0%)
>> 
>> The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec().
>> Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__() to debug.
>> 
>> ....etcetcetc. The process hangs here.
>> 
>> I get the same messages with my own data. I must have overlooked something. Any suggestions?
>> 
>> Dr David Iles
>> School of Biology
>> University of Leeds
>> Leeds LS2 9JT
>> 
>> d.e.iles at leeds.ac.uk<mailto:d.e.iles at leeds.ac.uk>
>> 
>>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>> 
>> attached base packages:
>> [1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>>  [1] RBGL_1.34.0          BiocInstaller_1.8.3  GSVAdata_0.99.9      hgu95a.db_2.8.0      org.Hs.eg.db_2.8.0
>>  [6] RSQLite_0.11.2       DBI_0.2-5            GSVA_1.6.1           GSEABase_1.20.1      annotate_1.36.0
>> [11] AnnotationDbi_1.20.3 Rgraphviz_2.2.1      graph_1.36.1         RColorBrewer_1.0-5   limma_3.14.3
>> [16] genefilter_1.40.0    Biobase_2.18.0       BiocGenerics_0.4.0
>> 
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.16.4  splines_2.15.2  stats4_2.15.2   survival_2.37-2 tools_2.15.2    XML_3.95-0.1    xtable_1.7-0
>> 
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>> 
> 
> -- 
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
> 
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